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Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface.
Chen, D, Chen, Z, Wei, GW
International journal for numerical methods in biomedical engineering. 2012;(1):25-51
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Abstract
Proton transport plays an important role in biological energy transduction and sensory systems. Therefore, it has attracted much attention in biological science and biomedical engineering in the past few decades. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins involving continuum, atomic, and quantum descriptions, assisted with the evolution, formation, and visualization of membrane channel surfaces. We describe proton dynamics quantum mechanically via a new density functional theory based on the Boltzmann statistics, while implicitly model numerous solvent molecules as a dielectric continuum to reduce the number of degrees of freedom. The density of all other ions in the solvent is assumed to obey the Boltzmann distribution in a dynamic manner. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic scale. A variational solute-solvent interface is designed to separate the explicit molecule and implicit solvent regions. We formulate a total free-energy functional to put proton kinetic and potential energies, the free energy of all other ions, and the polar and nonpolar energies of the whole system on an equal footing. The variational principle is employed to derive coupled governing equations for the proton transport system. Generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation, and generalized Kohn-Sham equation are obtained from the present variational framework. The variational solvent-solute interface is generated and visualized to facilitate the multiscale discrete/continuum/quantum descriptions. Theoretical formulations for the proton density and conductance are constructed based on fundamental laws of physics. A number of mathematical algorithms, including the Dirichlet-to-Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The gramicidin A channel is used to validate the performance of the proposed proton transport model and demonstrate the efficiency of the proposed mathematical algorithms. The proton channel conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and confirms the proposed model.
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[Structure and function of energy transduction protein complex of bacterial flagellar motor].
Terauchi, T, Kojima, S, Homma, M
Seikagaku. The Journal of Japanese Biochemical Society. 2011;(9):822-33
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Energy-converting [NiFe] hydrogenases from archaea and extremophiles: ancestors of complex I.
Hedderich, R
Journal of bioenergetics and biomembranes. 2004;(1):65-75
Abstract
[NiFe] hydrogenases are well-characterized enzymes that have a key function in the H2 metabolism of various microorganisms. In the recent years a subfamily of [NiFe] hydrogenases with unique properties has been identified. The members of this family form multisubunit membrane-bound enzyme complexes composed of at least four hydrophilic and two integral membrane proteins. These six conserved subunits, which built the core of these hydrogenases, have closely related counterparts in energy-conserving NADHquinone oxidoreductases (complex I). However, the reaction catalyzed by these hydrogenases differs significantly from the reaction catalyzed by complex I. For some of these hydrogenases the physiological role is to catalyze the reduction of H+ with electrons derived from reduced ferredoxins or poly-ferredoxins. This exergonic reaction is coupled to energy conservation by means of electron-transport phosphorylation. Other members of this hydrogenase family mainly function to provide the cell with reduced ferredoxin with H2 as electron donor in a reaction driven by reverse electron transport. As complex I these hydrogenases function as ion pumps and have therefore been designated as energy-converting [NiFe] hydrogenases.
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Dissimilatory oxidation and reduction of elemental sulfur in thermophilic archaea.
Kletzin, A, Urich, T, Müller, F, Bandeiras, TM, Gomes, CM
Journal of bioenergetics and biomembranes. 2004;(1):77-91
Abstract
The oxidation and reduction of elemental sulfur and reduced inorganic sulfur species are some of the most important energy-yielding reactions for microorganisms living in volcanic hot springs, solfataras, and submarine hydrothermal vents, including both heterotrophic, mixotrophic, and chemolithoautotrophic, carbon dioxide-fixing species. Elemental sulfur is the electron donor in aerobic archaea like Acidianus and Sulfolobus. It is oxidized via sulfite and thiosulfate in a pathway involving both soluble and membrane-bound enzymes. This pathway was recently found to be coupled to the aerobic respiratory chain, eliciting a link between sulfur oxidation and oxygen reduction at the level of the respiratory heme copper oxidase. In contrast, elemental sulfur is the electron acceptor in a short electron transport chain consisting of a membrane-bound hydrogenase and a sulfur reductase in (facultatively) anaerobic chemolithotrophic archaea Acidianus and Pyrodictium species. It is also the electron acceptor in organoheterotrophic anaerobic species like Pyrococcus and Thermococcus, however, an electron transport chain has not been described as yet. The current knowledge on the composition and properties of the aerobic and anaerobic pathways of dissimilatory elemental sulfur metabolism in thermophilic archaea is summarized in this contribution.
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The critical power model for intermittent exercise.
Morton, RH, Billat, LV
European journal of applied physiology. 2004;(2-3):303-7
Abstract
This paper develops and illustrates the critical power model for intermittent work. Model theoretic development reveals that total endurance time is always a step function of one or more of the four independent variables: work interval power output ( P(w)), rest interval power output ( P(r)), work interval duration ( t(w)), and rest interval duration ( t(r)). Six endurance-trained male athletes recorded their best performances during the season in 3-, 5-, and 10-km races, and performed three different intermittent running tests to exhaustion in random order, recording their total endurance times. These data were used to illustrate the model and compare anaerobic distance capacities (alpha) and critical velocities (beta) estimated from each type of exercise. Good fits of the model to data were obtained in all cases: 0.954< R(2)<0.999. Critical velocity was found to be significantly less when estimated using an intermittent versus continuous running protocol.
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6.
Touch and go: tying TonB to transport.
Postle, K, Kadner, RJ
Molecular microbiology. 2003;(4):869-82
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Abstract
The TonB system of Gram-negative bacteria appears to exist for the purpose of transducing the protonmotive force energy from the cytoplasmic membrane, where it is generated, to the outer membrane, where it is needed for active transport of iron siderophores, vitamin B12 and, in pathogens, iron from host-binding proteins. In this review, we bring the reader up to date on the developments in the field since the authors each wrote reviews in this journal in 1990.
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7.
Effects of daily activity recorded by pedometer on peak oxygen consumption (VO2peak), ventilatory threshold and leg extension power in 30- to 69-year-old Japanese without exercise habit.
Zhang, JG, Ohta, T, Ishikawa-Takata, K, Tabata, I, Miyashita, M
European journal of applied physiology. 2003;(1-2):109-13
Abstract
The relationships among walk steps, exercise habits and peak oxygen consumption (VO2peak), ventilatory threshold (VT) and leg extension power (LEP) were examined in 709 apparently healthy Japanese subjects (male 372, female 337) aged 30-69 years. Walk steps were evaluated using a pedometer. VO2peak and VT were assessed by a cycle ergometer test, while LEP was measured with an isokinetic leg extension system (Combi, Anaero Press 3500, Japan). Subjects who participated in exercise three times or more a week demonstrated significantly greater VO2peak and VT when compared with subjects without exercise habits. When a separate analysis was conducted on subjects who exercised fewer than three times per week, we found that the subgroup with the highest number of walk steps showed significantly greater VT in all male subjects and female subjects aged 30-49 years, but a significantly greater VO2peak only in females aged 30-49 years, when compared to the subgroup with the fewest walk steps. These results suggest that although some people exercise less than three times a week, if they are quite active in daily life, such activities might also confer benefits upon their fitness.
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Hand rim configuration: effects on physical strain and technique in unimpaired subjects?
van der Woude, LH, Formanoy, M, de Groot, S
Medical engineering & physics. 2003;(9):765-74
Abstract
OBJECTIVE Hand rim wheelchair propulsion is inefficient and physically straining. To evaluate the possibly advantageous role in this respect of three different prototype hand rim configurations (a rubber foam-coated cylindrical (II) hand rim and two profiled rubber foam-coated hand rims (wide and narrow: III, IV)), a group of 10 unimpaired subjects conducted four submaximal discontinuous wheelchair exercise tests on a computer-controlled wheelchair ergometer, thus allowing a comparison with a standard hand rim (chromium-plated round hand rim (I)). METHODS Apart from physiological measures (oxygen uptake, heart rate (HR), ventilation, mechanical efficiency (ME)), a subjective score for the rating of each of the hand rims was determined, as well as characteristics of the force application in the propulsion phase during each test condition. Timing parameters of the push and recovery phase were determined. Each exercise test was conducted with one of the four hand rim configurations in a counter-balanced order. RESULTS Analysis of variance with repeated measures (hand rim configuration, power output) revealed no significant effects (P>0.05) on any of the physiological parameters and force application characteristics for the main factor 'hand rim configuration'. Only the subjective score (scale 0-10) for rating of the hand rims proved significantly different between the round rubber (7.5+/-0.53) coated hand rim-receiving the highest score-versus the narrow rubber-coated flat profiled hand rim (5.5+/-1.72). DISCUSSION In this subject group and under the selected tasks and submaximal conditions of wheelchair propulsion, the studied hand rim configurations did not introduce critical shifts in the technique of (de-)coupling and power production in the push phase. As a consequence, no systematic shifts in ME are found among the different hand rim configurations. It is suggested that the biological constraints of the task overrule the possible effects of small design variations of the different hand rim configurations within the studied subject group and under the limited test conditions. The hand rim design characteristics may however be much more critical in (1) experienced wheelchair users, (2) especially those subjects with a limited hand-arm and/or trunk function and/or (3) under much more extreme conditions of daily wheelchair ambulation (i.e. turning, stopping/starting, negotiating a slope) or during peak performance. These issues clearly require continued future research. As such, the current results can be viewed as preliminary results only.
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Structural organization and energy transduction mechanism of Na+,K+-ATPase studied with transition metal-catalyzed oxidative cleavage.
Goldshleger, R, Patchornik, G, Shimon, MB, Tal, DM, Post, RL, Karlish, SJ
Journal of bioenergetics and biomembranes. 2001;(5):387-99
Abstract
This chapter describes contributions of transition metal-catalyzed oxidative cleavage of Na+,K+-ATPase to our understanding of structure-function relations. In the presence of ascorbate/H2O2, specific cleavages are catalyzed by the bound metal and because more than one peptide bond close to the metal can be cleaved, this technique reveals proximity of the different cleavage positions within the native structure. Specific cleavages are catalyzed by Fe2+ bound at the cytoplasmic surface or by complexes of ATP-Fe2+, which directs the Fe2+ to the normal ATP-Mg2+ site. Fe2+- and ATP-Fe2+-catalyzed cleavages reveal large conformation-dependent changes in interactions between cytoplasmic domains, involving conserved cytoplasmic sequences, and a change of ligation of Mg2+ ions between E1P and E2P, which may be crucial in facilitating hydrolysis of E2P. The pattern of domain interactions in E1 and E2 conformations, and role of Mg2+ ions, may be common to all P-type pumps. Specific cleavages can also be catalyzed by Cu2+ ions, bound at the extracellular surfaces, or a hydrophobic Cu2+-diphenyl phenanthroline (DPP) complex, which directs the Cu2+ to the membrane-water interface. Cu2+ or Cu2+-DPP-catalyzed cleavages are providing information on alpha/beta subunit interactions and spatial organization of transmembrane segments. Transition metal-catalyzed cleavage could be widely used to investigate other P-type pumps and membrane proteins and, especially, ATP binding proteins.
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10.
Effects of external loading on power output in a squat jump on a force platform: a comparison between strength and power athletes and sedentary individuals.
Driss, T, Vandewalle, H, Quièvre, J, Miller, C, Monod, H
Journal of sports sciences. 2001;(2):99-105
Abstract
The aim of this study was to determine the effects of external loading on power output during a squat jump on a force platform in athletes specializing in strength and power events (6 elite weight-lifters and 16 volleyball players) and in 20 sedentary individuals. Instantaneous power was computed from time-force curves during vertical jumps with and without an external load (0, 5 or 10 kg worn in a special vest). The jumps were performed from a squat position, without lower limb counter-movement or an arm swing. Peak instantaneous power corresponded to the highest value of instantaneous power during jumping. Average power throughout the push phase of the jump was also calculated. A two-way analysis of variance showed significant interactions between the load and group effects for peak instantaneous power (P< 0.01) and average power (P< 0.001). Peak instantaneous power decreased significantly in sedentary individuals when moderate external loads were added. The peak instantaneous power at 0 kg was greater than that at 5 and 10 kg in the sedentary individuals. In contrast, peak instantaneous power was independent of load in the strength and power athletes. Mean power at 0 kg was significantly lower than at 5 kg in the athletes; at 0 kg it was significantly higher than at 10 kg in the sedentary males and at 5 and 10 kg in the sedentary females. In all groups, the force corresponding to peak instantaneous power increased and the velocity corresponding to peak instantaneous power decreased with external loading. The present results suggest that the effects of external loading on peak instantaneous power are not significant in strength and power athletes provided that the loads do not prevent peak velocity from being higher than the velocity that is optimal for maximal power output.